Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 184069 - new ebuild: sci-biology/sombrero
Summary: new ebuild: sci-biology/sombrero
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High enhancement (vote)
Assignee: Default Assignee for New Packages
URL: http://bioinf.nuigalway.ie/sombrero/
Whiteboard:
Keywords: EBUILD
Depends on:
Blocks:
 
Reported: 2007-07-03 09:51 UTC by dawe
Modified: 2010-06-30 18:04 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---

Attachments
the sombrero ebuild (sombrero-1.1.ebuild,761 bytes, text/plain)
2007-07-03 09:52 UTC, dawe 		Details
sombrero mpi version ebuild (sombrero-mpi-1.1.ebuild,794 bytes, text/plain)
2007-07-03 09:55 UTC, dawe 		Details
sombrero-1.1.ebuild (sombrero-1.1.ebuild,659 bytes, text/plain)
2007-07-25 06:38 UTC, Andrey Kislyuk (RETIRED) 		Details
View All Add an attachment (proposed patch, testcase, etc.)

Note You need to log in before you can comment on or make changes to this bug.
Description dawe 2007-07-03 09:51:33 UTC 
Sombrero is a new tool for motif discovery that uses SOM.
It is a small program, only 3 cpp files. It includes also two perl utilities to handle data.


Reproducible: Always
Comment 1 dawe 2007-07-03 09:52:52 UTC 
Created attachment 123747 [details]
the sombrero ebuild
Comment 2 dawe 2007-07-03 09:55:57 UTC 
Created attachment 123748 [details]
sombrero mpi version ebuild

Actually one can diff the normal and mpi sources and provide the diff as a patch to apply with a mpi IUSE flag...
Both the sources can be downloaded from the same group. 
I also know that this second ebuild can be proposed as a separate one. I think it depends on how you want to add it: I mean 
-clustalw style (two binaries, two ebuilds for mpi and non-mpi)
-mrbayes style (one ebuild with mpi flag)
Comment 3 dawe 2007-07-03 09:58:45 UTC 
I'm giving some emerge --info...
x86:

emerge --info
Portage 2.1.2.7 (default-linux/x86/no-nptl, gcc-4.1.1, glibc-2.5-r0, 2.6.19-gentoo-r4-smp i686)
=================================================================
System uname: 2.6.19-gentoo-r4-smp i686 Intel(R) Xeon(TM) CPU 3.06GHz
Gentoo Base System version 1.12.9
Timestamp of tree: Mon, 07 May 2007 09:20:01 +0000
dev-java/java-config: 1.3.7, 2.0.31-r3
dev-lang/python:     2.4.4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox:    1.2.18.1
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.9.6-r2, 1.10
sys-devel/binutils:  2.17
sys-devel/gcc-config: 1.3.14
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.19.2-r1
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=pentium4 -O2 -fomit-frame-pointer -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/terminfo /etc/texmf/web2c"
CXXFLAGS="-march=pentium4 -O2 -fomit-frame-pointer -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="X apm arts berkdb bitmap-fonts cli cracklib crypt cups dri eds emboss encode foomaticdb fortran gdbm gif gpm gstreamer gtk gtk2 iconv imlib ipv6 isdnlog jpeg kde ldap libg++ libwww mad midi mikmod motif mp3 mpeg mysql ncurses nls ogg opengl oss pam pcre perl png pppd python qt3 qt4 quicktime readline reflection session spell spl ssl tcpd threads truetype truetype-fonts type1-fonts vorbis x86 xml xorg xv zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="apm ark ati chips cirrus cyrix dummy fbdev glint i128 i740 i810 imstt mga neomagic nsc nv rendition s3 s3virge savage siliconmotion sis sisusb tdfx tga trident tseng v4l vesa vga via vmware voodoo"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 4 dawe 2007-07-03 09:59:09 UTC 
amd64:
emerge --info
Portage 2.1.2.7 (default-linux/amd64/2006.1, gcc-4.1.1, glibc-2.4-r4, 2.6.15-gentoo-r7-smp x86_64)
=================================================================
System uname: 2.6.15-gentoo-r7-smp x86_64 AMD Opteron(tm) Processor 252
Gentoo Base System version 1.6.12
Timestamp of tree: Mon, 07 May 2007 09:30:10 +0000
dev-java/java-config: 1.3.7, 2.0.32
dev-lang/python:     2.3.5-r3, 2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox:    1.2.18.1
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.17
sys-devel/gcc-config: 1.3.13-r4
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-mtune=k8 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib/X11/xkb"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c"
CXXFLAGS="-mtune=k8 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoaddcvs ccache distcc distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="amd64 berkdb bitmap-fonts cli cracklib crypt cups dri fortran gdbm gpm iconv ipv6 isdnlog libg++ midi ncurses nls nptl nptlonly pam pcre perl ppds pppd python readline reflection session spl ssl tcpd threads truetype-fonts type1-fonts unicode xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="apm ark ati chips cirrus cyrix dummy fbdev glint i128 i810 mga neomagic nv rendition s3 s3virge savage siliconmotion sis sisusb tdfx tga trident tseng v4l vesa vga via vmware voodoo"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

ia64:
emerge --info
Portage 2.1.2.7 (default-linux/ia64/2006.0, gcc-4.1.1, glibc-2.4-r4, 2.6.17-gentoo-r3-smp ia64)
=================================================================
System uname: 2.6.17-gentoo-r3-smp ia64 Itanium 2
Gentoo Base System version 1.12.5
Timestamp of tree: Mon, 07 May 2007 09:00:01 +0000
dev-java/java-config: 1.3.7, 2.0.30
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox:    1.2.18.1
sys-devel/autoconf:  2.61
sys-devel/automake:  1.4_p6, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.17
sys-devel/gcc-config: 1.3.13-r4
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r6
ACCEPT_KEYWORDS="ia64 x86 ~ia64"
AUTOCLEAN="yes"
CBUILD="ia64-unknown-linux-gnu"
CFLAGS="-mtune=itanium2 -O2 -pipe -ffast-math"
CHOST="ia64-unknown-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c"
CXXFLAGS="-mtune=itanium2 -O2 -pipe -ffast-math"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="berkdb bitmap-fonts cli cracklib crypt cups dri eds encode foomaticdb fortran gdbm gif gnome gpm gstreamer gtk gtk2 ia64 iconv imlib ipv6 isdnlog jpeg kde libg++ libwww midi mikmod motif mysql ncurses nls nptl nptlonly ogg opengl oss pam pcre perl png pppd python qt3 qt4 quicktime readline reflection sdl session spell spl ssl tcpd threads truetype truetype-fonts type1-fonts vorbis xml2 xorg xv zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="apm ark ati chips cirrus cyrix dummy fbdev glint i128 i740 i810 imstt mga neomagic nv rendition s3 s3virge savage siliconmotion sisusb tdfx tga v4l vesa vga via voodoo"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 5 dawe 2007-07-03 09:59:19 UTC 

alpha 2.4:
emerge --info
Portage 2.1.2.2 (default-linux/alpha/no-nptl/2.4, gcc-3.4.6, glibc-2.3.5-r3, 2.4.30 alpha)
=================================================================
System uname: 2.4.30 alpha EV68CB
Gentoo Base System version 1.6.15
Timestamp of tree: Mon, 07 May 2007 09:29:01 +0000
dev-lang/python:     2.3.5, 2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.13-r3
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.4.26-r1
ACCEPT_KEYWORDS="alpha"
AUTOCLEAN="yes"
CBUILD="alphaev67-unknown-linux-gnu"
CFLAGS="-mieee -mcpu=ev67 -Wa,-mev6 -O2 -pipe "
CHOST="alphaev67-unknown-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-mieee -mcpu=ev67 -Wa,-mev6 -O2 -pipe "
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="alpha apache2 arts berkdb bitmap-fonts cli cracklib crypt cups dri eds encode esd foomaticdb fortran gdbm gif gnome gpm gstreamer gtk gtk2 iconv imlib ipv6 isdnlog jpeg kde libg++ libwww mad midi mikmod motif mp3 mpeg mysql ncurses nls ogg opengl oss pam pcre perl png pppd python qt3 qt4 quicktime readline reflection sdl session spell spl ssl tcpd threads truetype truetype-fonts type1-fonts vorbis xml xorg xv zlib" ALSA_CARDS="ali5451 als4000 bt87x ca0106 cmipci emu10k1 ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 maestro3 trident usb-audio via82xx ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="cirrus ati dummy fbdev glint mga nv rendition s3 s3virge savage siliconmotion sisusb tdfx tga v4l vga voodoo"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS


alpha 2.6:
emerge --info
Portage 2.1.2.2 (default-linux/alpha/2006.1, gcc-3.4.6, glibc-2.3.6-r4, 2.6.16.19 alpha)
=================================================================
System uname: 2.6.16.19 alpha EV68AL
Gentoo Base System version 1.12.5
Timestamp of tree: Mon, 07 May 2007 09:30:10 +0000
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.6.3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.13-r4
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r4
ACCEPT_KEYWORDS="alpha"
AUTOCLEAN="yes"
CBUILD="alphaev67-unknown-linux-gnu"
CFLAGS="-mieee -mcpu=ev67 -Wa,-mev6 -O2 -pipe "
CHOST="alphaev67-unknown-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/terminfo"
CXXFLAGS="-mieee -mcpu=ev67 -Wa,-mev6 -O2 -pipe "
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="alpha berkdb bitmap-fonts cli cracklib crypt cups dri fortran gdbm iconv ipv6 isdnlog ldap libg++ midi ncurses nls nptl nptlonly pam pcre perl ppds pppd python readline reflection session spl ssl tcpd threads truetype truetype-fonts type1-fonts unicode xml xorg zlib" ALSA_CARDS="ali5451 als4000 bt87x ca0106 cmipci emu10k1 ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 maestro3 trident usb-audio via82xx ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="cirrus ati dummy fbdev glint mga nv rendition s3 s3virge savage siliconmotion sisusb tdfx tga v4l vga voodoo"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 6 Andrey Kislyuk (RETIRED) gentoo-dev 2007-07-25 06:38:02 UTC 
Created attachment 125955 [details]
sombrero-1.1.ebuild

Beautified ebuild.

Please read http://devmanual.gentoo.org/
Comment 7 Andreas K. Hüttel archtester gentoo-dev 2010-06-30 18:04:51 UTC 
Current version is 1.1 (2007)